Research workbench
Crystal structure of glyceraldehyde-3-phosphate dehydrogenase complexed with CP12 in the presence of copper from synechococcus elongatus
Analyse Crystal structure of glyceraldehyde-3-phosphate dehydrogenase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B1J
- Type
- protein
- Length
- 721 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde 3-phosphate dehydrogenase (NADP+); CP12
- EC
- 1.2.1.13
- UniProt
- Q9R6W2, Q6BBK3
- Ligands
- NAD, CU
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glyceraldehyde 3-phosphate dehydrogenase (NADP+) (EC 1.2.1.13) | protein | 338 | 29% helix, 28% strand | Q9R6W2 |
| C | CP12 | protein | 22 | 32% helix, 0% strand | Q6BBK3 |
| D | CP12 | protein | 23 | 30% helix, 0% strand | Q6BBK3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C, B, D
- CU · Copper (II) ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.75 | 0.81 | 85 | NAD |
| 2 | 651 | 0.73 | 0.80 | 79 | NAD |
| 3 | 328 | 0.54 | 0.74 | 50 | empty |
| 4 | 82 | 0.36 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–D · 857 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 798 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 570 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3B1J · Crystal structure of Glyceraldehyde-3-Phosphate Dehydrogenase complexed with CP12 in the… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9R6W2
- Every structure of UniProt Q6BBK3
- Elsewhere: RCSB PDB 3B1J · PDBe 3B1J · UniProt Q9R6W2 · UniProt Q6BBK3
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